Drug discovery and drug screening in the chemical and biological arts commonly involve performing assays on very large numbers of compounds or molecules. These assays typically include screening chemical libraries for compounds of interest, screening for particular target molecules in test samples, and testing generally for chemical and biological interactions of interest between molecules. The assays described above often require carrying out thousands of individual chemical or biological reactions. For example, a drug discovery assay may involve testing thousands of compounds against a specific target analyte. Any compounds that are observed to react, bind, or otherwise interact with the target analyte may hold promise for any number of utilities where the observed interaction is believed to be of significance.
A number of practical problems exist in the handling of the large number of individual reactions required in the assays described above. Perhaps the most significant problem is the necessity to label and track each reaction. For example, if a reaction of interest is observed in only one in a group of thousands of reactions, the researcher must be able to determine which one of the thousands of initial compounds or molecules produced that reaction.
One conventional method of tracking the identity of the reactions is by physically separating each reaction into an individual reaction vessel within a high-density array and maintaining a record of what individual reactants were used in each vessel. Thus, for example, when a reaction of interest is observed in a vessel labeled as number 5 of 1000, the researcher can refer to the record of reactants used in the vessels and will learn from the record of vessel 5 what specific reactants were present to lead to the reaction of interest. Examples of the high-density arrays referred to above are 384-, 864-, 1,536-, 3,456-, and 9,600-well microtiter plate containers, where each well of a microtiter plate constitutes a miniature reaction vessel. Miniaturized reaction wells are used because they conserve space and reduce the cost of reagents used in the assays.
The use of microtiter plate containers in chemical and biological assays, however, carries a number of disadvantages. For example, the use of the plates requires carefully separating a very large number of discrete reaction vessels, rather than allowing for all reactions to take place freely, and often more conveniently, in one reaction vessel. Furthermore, the requirement that the reaction volumes be spatially separated carries with it a physical limitation to the size of microtiter plate used, and thus to the number of different reactions that may be carried out on the plate.
In light of the limitations described above in the use of microtiter plates, some attempts have been made to develop other means of tracking individual reactions in high-throughput assays. These methods have abandoned the concept of spatially separating the reactions, and instead track the individual reactions by other means. For example, methods have been developed to carry out high-throughput assays and reactions on microcarriers as supports. Each microcarrier may contain one particular ligand bound to its surface to act as a reactant, and the microcarrier can additionally contain a “code” that identifies the microcarrier and therefore identifies the particular ligand bound to its surface. These methods described above allow for “random processing,” which means that thousands of uniquely coded microcarriers, each having a ligand bound to their surface, may all be mixed and subjected to an assay simultaneously. Those microcarriers that show a favorable reaction of interest between the attached ligand and target analyte may then have their code read, thereby leading to the identity of the ligand that produced the favorable reaction.
The practice of random processing described above requires accurate encoding of each of the microcarriers separately, and requires accurate and consistent identification of the codes. Because assays using random processing rely heavily on the coding of the microcarriers for their results, the quality of the assays depends largely on the quality and readability of the codes on the microcarriers. Attempts to code microcarriers are still limited to differential coloring (Dye-Trak microspheres), fluorescent labeling (Fluorospheres; Nu-flow), so-called remotely programmable matrices with memories (IRORI; U.S. Pat. No. 5,751,629), detachable tags such as oligonucleotides and small peptides (U.S. Pat. No. 5,565,324; U.S. Pat. No. 5,721,099; U.S. Pat. No. 5,789,172), and solid phase particles that carry transponders (U.S. Pat. No. 5,736,332). The disclosures of the patents cited above are incorporated by reference herein.
These known methods identified above for coding microcarriers each carry disadvantages. For example, microcarriers that are differentiated solely on the basis of their size, shape, color, fluorescence intensity, or combinations thereof often cannot provide enough unique readable combinations of those variables to create the massive number of unique codes necessary to accompany the testing of a correspondingly large number of different molecules. In addition, any microcarriers carrying foreign bodies on their surface to serve as the codes, such as detachable tags or fluorescent markers, run the risk that the attached moieties may interfere with the binding or reaction of the ligand-bound molecules on the microcarriers that target the analytes in the assays. After the separation of the microcarriers of interest that exhibit a favorable reaction, methods of encoding microcarriers with detachable tags also often involve the additional step of cleaving and analyzing the tags to ultimately learn the identity of the underlying ligands on the microcarriers that produced the favorable reactions. This cleaving step naturally extends the time and effort necessary to determine the results of the tests.
In light of the above, there remains in the art a need for simple ways for identifying single microcarriers in a massive population of otherwise identical microcarriers, especially ways for encoding a larger number of unique codes that need not be attached as foreign bodies to the surfaces of the microcarriers.